Sun, 04 Sep 2022

Package systemfit updated to version 1.1-28 with previous version 1.1-26 dated 2022-06-21

Title: Estimating Systems of Simultaneous Equations
Description: Econometric estimation of simultaneous systems of linear and nonlinear equations using Ordinary Least Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS) as suggested, e.g., by Zellner (1962) <doi:10.2307/2281644>, Zellner and Theil (1962) <doi:10.2307/1911287>, and Schmidt (1990) <doi:10.1016/0304-4076(90)90127-F>.
Author: Arne Henningsen and Jeff D. Hamann
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

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Package sspse updated to version 1.0.3 with previous version 1.0.2 dated 2022-08-28

Title: Estimating Hidden Population Size using Respondent Driven Sampling Data
Description: Estimate the size of a networked population based on respondent-driven sampling data. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data. See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923> and Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>.
Author: Mark S. Handcock [aut, cre, cph], Krista J. Gile [aut, cph], Brian Kim [ctb], Katherine R. McLaughlin [ctb]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>

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Package nanonext updated to version 0.5.5 with previous version 0.5.4 dated 2022-09-02

Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library providing high-performance scalability protocols, implementing a cross-platform standard for messaging and communications. Serves as a concurrency framework for building distributed applications, utilising 'Aio' objects which automatically resolve upon completion of asynchronous operations.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package casen updated to version 0.2.1 with previous version 0.2.0 dated 2022-06-21

Title: Metodos De Estimacion Con Disenio Probabilistico y Estratificado en Encuesta CASEN (Estimation Methods with Probabilistic Stratified Sampling in CASEN Survey)
Description: Funciones para realizar estadistica descriptiva e inferencia con el disenio complejo de la Encuesta CASEN (Encuesta de Caracterizacion Socio-Economica). Incluye datasets que permiten armonizar los codigos de comunas que cambian entre anios y permite convertir a los codigos oficiales de SUBDERE. (Functions to compute descriptive and inferential statistics with CASEN Survey [Socio-Economic Characterization Survey] complex design. Includes datasets to harmonize commune codes that change across years and allows to convert to official SUBDERE codes.)
Author: Mauricio Vargas [aut, cre] , Ricardo Aravena [ths], Klaus Lehmann [ctb], Pontificia Universidad Catolica de Chile [cph], Ministerio de Desarrollo Social [dtc], Subsecretaria de Desarrollo Regional [dtc]
Maintainer: Mauricio Vargas <hello+r@pacha.dev>

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Package afttest updated to version 4.2.1.1 with previous version 4.2.1 dated 2022-08-29

Title: Model Diagnostics for Accelerated Failure Time Models
Description: A collection of model checking methods for semiparametric accelerated failure time (AFT) models under the rank-based approach. For the (computational) efficiency, Gehan's weight is used. It provides functions to verify whether the observed data fit the specific model assumptions such as a functional form of each covariate, a link function, and an omnibus test. The p-value offered in this package is based on the Kolmogorov-type supremum test and the variance of the proposed test statistics is estimated through the re-sampling method. Furthermore, a graphical technique to compare the shape of the observed residual to a number of the approximated realizations is provided.
Author: WooJung Bae [aut, cre], Dongrak Choi [aut], Sangwook Kang [aut]
Maintainer: WooJung Bae <matt.woojung@gmail.com>

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Package spBFA updated to version 1.2 with previous version 1.1 dated 2021-04-27

Title: Spatial Bayesian Factor Analysis
Description: Implements a spatial Bayesian non-parametric factor analysis model with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC). Spatial correlation is introduced in the columns of the factor loadings matrix using a Bayesian non-parametric prior, the probit stick-breaking process. Areal spatial data is modeled using a conditional autoregressive (CAR) prior and point-referenced spatial data is treated using a Gaussian process. The response variable can be modeled as Gaussian, probit, Tobit, or Binomial (using Polya-Gamma augmentation). Temporal correlation is introduced for the latent factors through a hierarchical structure and can be specified as exponential or first-order autoregressive. Full details of the package can be found in the accompanying vignette. Furthermore, the details of the package can be found in "Bayesian Non-Parametric Factor Analysis for Longitudinal Spatial Surfaces", by Berchuck et al (2019), <arXiv:1911.04337>. The paper is in press at the jo [...truncated...]
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>

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Package bmscstan updated to version 1.2.1.0 with previous version 1.1.0 dated 2020-11-08

Title: Bayesian Multilevel Single Case Models using 'Stan'
Description: Analyse single case analyses against a control group. Its purpose is to provide a flexible, with good power and low first type error approach that can manage at the same time controls' and patient's data. The use of Bayesian statistics allows to test both the alternative and null hypothesis. Scandola, M., & Romano, D. (2020, August 3). <doi:10.31234/osf.io/sajdq> Scandola, M., & Romano, D. (2021). <doi:10.1016/j.neuropsychologia.2021.107834>.
Author: Michele Scandola [aut, cre]
Maintainer: Michele Scandola <michele.scandola@univr.it>

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Package rticulate updated to version 1.7.3 with previous version 1.7.2 dated 2021-01-11

Title: Ultrasound Tongue Imaging
Description: A tool for processing Articulate Assistant Advanced™ (AAA) export files and plot tongue contour data from any system.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>

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Package smoothHR updated to version 1.0.4 with previous version 1.0.3 dated 2021-10-07

Title: Smooth Hazard Ratio Curves Taking a Reference Value
Description: Provides flexible hazard ratio curves allowing non-linear relationships between continuous predictors and survival. To better understand the effects that each continuous covariate has on the outcome, results are ex pressed in terms of hazard ratio curves, taking a specific covariate value as reference. Confidence bands for these curves are also derived.
Author: Artur Araujo [aut, cre] , Luis Meira-Machado [aut]
Maintainer: Artur Araujo <artur.stat@gmail.com>

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Package hunspell updated to version 3.0.2 with previous version 3.0.1 dated 2020-12-09

Title: High-Performance Stemmer, Tokenizer, and Spell Checker
Description: Low level spell checker and morphological analyzer based on the famous 'hunspell' library <https://hunspell.github.io>. The package can analyze or check individual words as well as parse text, latex, html or xml documents. For a more user-friendly interface use the 'spelling' package which builds on this package to automate checking of files, documentation and vignettes in all common formats.
Author: Jeroen Ooms [aut, cre], Authors of libhunspell [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package statgenIBD updated to version 1.0.5 with previous version 1.0.4 dated 2022-03-07

Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (<https://www.jstor.org/stable/29713>) and Huang (<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Author: Martin Boer [aut] , Bart-Jan van Rossum [aut, cre] , Wenhao Li [ctb] , Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Package rvinecopulib updated to version 0.6.2.1.1 with previous version 0.6.2.1.0 dated 2022-08-26

Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine copula modeling. The 'rvinecopulib' package implements the core features of the popular 'VineCopula' package, in particular inference algorithms for both vine copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker and more modern API, improved performances, especially in high dimensions, nonparametric and multi-parameter families, and the ability to model discrete variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only C++ library (currently version 0.6.2). Thus users do not need to install 'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre], Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>

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Package pmetar updated to version 0.4.0 with previous version 0.3.3 dated 2022-03-08

Title: Processing METAR Weather Reports
Description: Allows to download current and historical METAR weather reports extract and parse basic parameters and present main weather information. Current reports are downloaded from Aviation Weather Center <https://www.aviationweather.gov/metar> and historical reports from Iowa Environmental Mesonet web page of Iowa State University ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>.
Author: Pawel Cwiek [aut, cre], David Megginson [ctb] , Greg Thompson [ctb]
Maintainer: Pawel Cwiek <prc.altodato@gmail.com>

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Package lpSolve updated to version 5.6.16 with previous version 5.6.15 dated 2020-01-24

Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between lpSolve versions 5.6.15 dated 2020-01-24 and 5.6.16 dated 2022-09-04

 DESCRIPTION         |    6 +++---
 MD5                 |   10 +++++-----
 man/lp.Rd           |    6 +++---
 man/lp.assign.Rd    |    2 +-
 man/lp.transport.Rd |    2 +-
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 6 files changed, 17 insertions(+), 13 deletions(-)

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New package kernelboot with initial version 0.1.9
Package: kernelboot
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Version: 0.1.9
Date: 2022-08-25
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Description: Smoothed bootstrap and functions for random generation from univariate and multivariate kernel densities. It does not estimate kernel densities.
License: GPL-2
URL: https://github.com/twolodzko/kernelboot
BugReports: https://github.com/twolodzko/kernelboot/issues
Depends: R (>= 3.1.0)
LinkingTo: Rcpp
Imports: Rcpp, future, future.apply, parallelly
Suggests: covr, testthat, ks, KernSmooth, cramer
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-08-25 11:57:33 UTC; tymek
Repository: CRAN
Date/Publication: 2022-09-04 14:20:02 UTC

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New package GeoModels with initial version 1.0.2
Package: GeoModels
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis
Version: 1.0.2
Date: 2022-08-10
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Depends: R (>= 4.0.5), GPvecchia,fields, mapproj, shape, codetools
License: GPL (>= 3)
Encoding: UTF-8
Imports: methods, spam, scatterplot3d, dfoptim, dotCall64, optimParallel, parallel, plotrix, pracma, pbivnorm, zipfR, sn, nabor, numDeriv, hypergeo, ucminf, lamW, GpGp,VGAM, data.table
Suggests: actuar, GoFKernel
Repository: CRAN
URL: https://vmoprojs.github.io/GeoModels-page/
BugReports: https://github.com/vmoprojs/GeoModels/issues
NeedsCompilation: yes
Packaged: 2022-08-25 14:53:14 UTC; victormorales
Author: Moreno Bevilacqua [aut, cre] , Victor Morales-Onate [aut] , Christian Caamano-Carrillo [aut]
Date/Publication: 2022-09-04 14:30:16 UTC

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New package fastGLCM with initial version 1.0.1
Package: fastGLCM
Title: 'GLCM' Texture Features
Version: 1.0.1
Date: 2022-08-27
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
BugReports: https://github.com/mlampros/fastGLCM/issues
URL: https://github.com/mlampros/fastGLCM
Description: Two 'Gray Level Co-occurrence Matrix' ('GLCM') implementations are included: The first is a fast 'GLCM' feature texture computation based on 'Python' 'Numpy' arrays ('Github' Repository, <https://github.com/tzm030329/GLCM>). The second is a fast 'GLCM' 'RcppArmadillo' implementation which is parallelized (using 'OpenMP') with the option to return all 'GLCM' features at once. For more information, see "Artifact-Free Thin Cloud Removal Using Gans" by Toizumi Takahiro, Zini Simone, Sagi Kazutoshi, Kaneko Eiji, Tsukada Masato, Schettini Raimondo (2019), IEEE International Conference on Image Processing (ICIP), pp. 3596-3600, <doi:10.1109/ICIP.2019.8803652>.
SystemRequirements: apt-get-pip: apt-get install -y python3-pip (deb), python3-pip: python3 -m pip install -U pip (deb), numpy: pip3 install -U numpy (deb), cv2: pip3 install -U opencv-python (deb), matplotlib: pip3 install -U matplotlib (deb), skimage: pip3 install -U scikit-image (deb), libarmadillo: apt-get install -y libarmadillo-dev (deb), libblas: apt-get install -y libblas-dev (deb), liblapack: apt-get install -y liblapack-dev (deb), libarpack++2: apt-get install -y libarpack++2-dev (deb), gfortran: apt-get install -y gfortran (deb)
License: GPL-3
Copyright: inst/COPYRIGHTS
Depends: R(>= 3.2.3)
Imports: Rcpp (>= 1.0.8.3), R6, rlang, OpenImageR, utils
LinkingTo: Rcpp, RcppArmadillo, OpenImageR
Suggests: reticulate, covr, knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-08-27 15:51:08 UTC; lampros
Author: Lampros Mouselimis [aut, cre] , Takahiro Toizumi [cph]
Repository: CRAN
Date/Publication: 2022-09-04 14:30:05 UTC

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New package ecolMod with initial version 1.2.6.3
Package: ecolMod
Version: 1.2.6.3
Date: 2022-08-24
Title: "A Practical Guide to Ecological Modelling - Using R as a Simulation Platform"
Author: Karline Soetaert <karline.soetaert@nioz.nl>, Peter MJ Herman <peter.herman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Depends: R (>= 2.01), rootSolve, shape, diagram, deSolve
Imports: stats, graphics, grDevices
Suggests: maps, seacarb, scatterplot3d, deldir
Description: Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer. All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11. The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter. Solutions to model projects are in the same subdirectories.
License: GPL (>= 2)
LazyData: yes
NeedsCompilation: yes
Packaged: 2022-08-24 10:53:41 UTC; karlines
Repository: CRAN
Date/Publication: 2022-09-04 14:20:05 UTC

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Package conos updated to version 1.4.7 with previous version 1.4.6 dated 2022-04-11

Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

Diff between conos versions 1.4.6 dated 2022-04-11 and 1.4.7 dated 2022-09-04

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Package changepoints updated to version 1.1.0 with previous version 1.0.0 dated 2021-12-10

Title: A Collection of Change-Point Detection Methods
Description: Performs a series of offline and/or online change-point detection algorithms for 1) univariate mean: <doi:10.1214/20-EJS1710>, <arXiv:2006.03283>; 2) univariate polynomials: <doi:10.1214/21-EJS1963>; 3) univariate and multivariate nonparametric settings: <doi:10.1214/21-EJS1809>, <doi:10.1109/TIT.2021.3130330>; 4) high-dimensional covariances: <doi:10.3150/20-BEJ1249>; 5) high-dimensional networks with and without missing values: <doi:10.1214/20-AOS1953>, <arXiv:2101.05477>, <arXiv:2110.06450>; 6) high-dimensional linear regression models: <arXiv:2010.10410>, <arXiv:2207.12453>; 7) high-dimensional vector autoregressive models: <arXiv:1909.06359>; 8) high-dimensional self exciting point processes: <arXiv:2006.03572>; 9) dependent dynamic nonparametric random dot product graphs: <arXiv:1911.07494>; 10) univariate mean against adversarial attacks: <arXiv:2105.10417>.
Author: Haotian Xu [aut, cre], Oscar Padilla [aut], Daren Wang [aut], Mengchu Li [aut], Qin Wen [ctb]
Maintainer: Haotian Xu <haotian.xu@uclouvain.be>

Diff between changepoints versions 1.0.0 dated 2021-12-10 and 1.1.0 dated 2022-09-04

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Package causalOT updated to version 0.1.2 with previous version 0.1 dated 2022-03-14

Title: Optimal Transport Weights for Causal Inference
Description: Uses optimal transport distances to find probabilistic matching estimators for causal inference. These methods are described in Dunipace, Eric (2021) <arXiv:2109.01991>. The package will build the weights, estimate treatment effects, and calculate confidence intervals via the methods described in the paper. The package also supports several other methods as described in the help files.
Author: Eric Dunipace [aut, cre]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>

Diff between causalOT versions 0.1 dated 2022-03-14 and 0.1.2 dated 2022-09-04

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Package BoolNet updated to version 2.1.7 with previous version 2.1.5 dated 2019-04-16

Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
Author: Christoph Muessel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] , Troy D. Hanson [ctb]
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>

Diff between BoolNet versions 2.1.5 dated 2019-04-16 and 2.1.7 dated 2022-09-04

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Package lazyraster (with last version 0.5.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-10-07 0.5.1
2019-10-09 0.5.0

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Package bpcs (with last version 1.0.0) was removed from CRAN

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Package tidymv updated to version 3.3.2 with previous version 3.3.1 dated 2022-04-18

Title: Tidy Model Visualisation for Generalised Additive Models
Description: Provides functions for visualising generalised additive models and getting predicted values using tidy tools from the 'tidyverse' packages.
Author: Stefano Coretta [aut, cre], Jacolien van Rij [cph] , Martijn Wieling [cph]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>

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Package speakr updated to version 3.2.1 with previous version 3.2.0 dated 2021-07-22

Title: A Wrapper for the Phonetic Software 'Praat'
Description: It allows running 'Praat' scripts from R and it provides some wrappers for basic plotting. It also adds support for literate markdown tangling. The package is designed to bring reproducible phonetic research into R.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>

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Package fcaR updated to version 1.2.0 with previous version 1.1.1 dated 2021-06-28

Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems.
Author: Domingo Lopez Rodriguez [aut, cre] , Angel Mora [aut], Jesus Dominguez [aut], Ana Villalon [aut], Ian Johnson [ctb]
Maintainer: Domingo Lopez Rodriguez <dominlopez@uma.es>

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Package economiccomplexity updated to version 1.4.0 with previous version 1.1 dated 2020-09-19

Title: Computational Methods for Economic Complexity
Description: A wrapper of different methods from Linear Algebra for the equations introduced in The Atlas of Economic Complexity and related literature. This package provides standard matrix and graph output that can be used seamlessly with other packages. See <doi:10.21105/joss.01866> for a summary of these methods and its evolution in literature.
Author: Mauricio Vargas [aut, cre, cph] , Carlo Bottai [ctb] , Diego Kozlowski [ctb] , Nico Pintar [rev] , The World Bank [dtc] , Open Trade Statistics [dtc]
Maintainer: Mauricio Vargas <hello+r@pacha.dev>

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Package gRain updated to version 1.3.11 with previous version 1.3.10 dated 2022-05-10

Title: Graphical Independence Networks
Description: Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems. Documentation of the package is provided in vignettes included in the package and in the paper by Højsgaard (2012, <doi:10.18637/jss.v046.i10>). See 'citation("gRain")' for details.
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>

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